This is a simple issue, but it bothered me to no end, so let me pay it forward. 😉
I recently started using Mountain Lion Mission Control (Spaces) more often and noticed an annoying little trend… it rearranges them.
Now when I use Spaces, I assign apps to different locations for a purpose. That purpose is so that I can compartmentalize my tasks. Mail? Space 1. Writing? Space 6. Terminal work? Space 3.
Mountain Lion (and Lion as of 10.7.2) poops all over that.
NOTE: To get here, go to the Apple in the top left corner of your screen, System Preferences, and select Mission Control (Spaces is controlled by Mission Control nowadays).
See the “Automatically rearrange spaces based on most recent use” checkbox? Disable that–like I did–and your Spaces won’t rearrange anymore.